4XNV: The human P2Y1 receptor

The human P2Y1 receptor in complex with BPTU. Determined by X-ray diffraction at 2.2 Å resolution. Released 1 Apr 2015.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Clostridium pasteurianum
Chains: 1
Atoms: 3,114
Mol. weight: 52.92 kDa
Ligands: BUR, CLR, Y01, OLC
Released: 1 Apr 2015

Explore 4XNV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XNV contains 18 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	50-78	29
β-strand	81	1	1
α-helix	85-112	28
α-helix	121-154	34
α-helix	161-183	23
α-helix	186-189	4
β-strand	191-194	4	2
β-strand	200-203	4	2
α-helix	211-222	12
α-helix	223-227	5
α-helix	228-245	18
α-helix	1001-1003	3
β-strand	1004-1006	3	3
β-strand	1012-1013	2	3
β-strand	1019	1	4
β-strand	1024	1	4
α-helix	1030-1032	3
α-helix	1046-1048	3
β-strand	1049-1051	3	3
α-helix	253-268	16
α-helix	269-273	5
α-helix	274-289	16
α-helix	293-295	3
α-helix	296-319	24
α-helix	321-326	6
α-helix	329-330	2
β-strand	333	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1	A	protein	421	Homo sapiens, Clostridium pasteurianum	P00268 (AlphaFold model), P47900 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4XNV_1 P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1 (chains A)
TEVLWPAVPNGTDAAFLAGPGSSWGNSTVASTAAVSSSFKCALTKTGFQFYYLPAVYILV
FIIGFLGNSVAIWMFVFHMKPWSGISVYMFNLALADFLYVLTLPALIFYYFNKTDWIFGD
AMCKLQRFIFHVNLYGSILFLTCISAHRYSGVVYPLKSLGRLKKKNAICISVLVWLIVVV
AISPILFYSGTGVRKNKTITCYDTTSDEYLRSYFIYSMCTTVAMFCVPLVLILGCYGLIV
RALIYKMKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE
PLRRKSIYLVIIVLTVFAVSYIPFHVMKTMNLRARLDFQTPAMCAFNDRVYATYQVTRGL
ASLNSCVNPILYFLAGDTFRRRLSRATRKASRRSEANLQSKSEDMTLNILPEFKQNGDTS
L

Ligands and cofactors

ID	Name	Formula	Copies
BUR	1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea	C23 H22 F3 N3 O3	1
CLR	Cholesterol	C27 H46 O	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	3
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	8
ZN	Zinc ion	Zn	1

Water and common crystallization additives (1PE) are not listed.

Primary citation

Two disparate ligand-binding sites in the human P2Y1 receptor. Zhang, D., Gao, Z.G., Zhang, K. et al. Nature (2015) 520:317-321. DOI 10.1038/nature14287 · PubMed

Other PDB entries of the same protein (UniProt P00268 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PVE 0.79 Å, NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of…
1IRO 1.1 Å, Rubredoxin (oxidized, fe(iii)) at 1.1 Å resolution
1IRN 1.2 Å, Rubredoxin (ZN-substituted) at 1.2 Å resolution
4RXN 1.2 Å, Crystallographic refinement of rubredoxin at 1.2 Å resolution
5RXN 1.2 Å, Combined crystallographic refinement and energy minimization of rubredoxin at 1.2 Å…
1SMM 1.36 Å, Crystal Structure of Cp Rd L41A mutant in oxidized state
1SMW 1.38 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 2 (soaked)
1SMU 1.43 Å, Crystal Structure of Cp Rd L41A mutant in reduced state 1 (drop-reduced)
1B13 1.5 Å, Clostridium pasteurianum rubredoxin G10A mutant
1FHH 1.5 Å, X-ray crystal structure of oxidized rubredoxin
1FHM 1.5 Å, X-ray crystal structure of reduced rubredoxin
1R0I 1.5 Å, cadmium-substituted rubredoxin

Browse structure collections

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